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4cefb9aa · Peter van 't Hof · e385f934 · 4cefb9aa
Commit 4cefb9aa authored 7 years ago by Peter van 't Hof
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -7,8 +7,10 @@ task FastqSplitter {

    command {
    mkdir -p ${sep=' ' prefix(outputPath + "/chunk_", chunks)}
-    ${if (numberChunks > 1) then ("java -jar " + tool_jar + " -I " + inputFastq + " -o ${sep=' -o ' chunks}")
-    else ("ln -sf " + inputFastq + " " + outputPath + "/chunk_0/" + basename(inputFastq))}
+    if [ ${numberChunks} -gt 1 ]; then
+        java -jar ${tool_jar} -I ${inputFastq} -o ${sep=' -o ' chunks}
+    else
+        ln -sf ${inputFastq} ${outputPath}/chunk_0/${basename(inputFastq)}
    }

    output {